<tool id="countNumber_parallel" name="countNumber (for DEA)">

	<description>Calculate the number of reads(annotations) overlapping for each transcript.</description>
	<command interpreter="python"> countNumber_parallel.py -i $inputTxt -o $outputTxt $tar $outputTarFile
	</command>

	<inputs>
		<param name="inputTxt" type="data" format="txt" label="Please choose your txt format file (which contains a list of gff3 overlapping results files)."/>		
		<param name="tar" type="boolean" truevalue="-t" falsevalue="" checked="False" label="tar option" help="This option creates a tar file for all out results" />
	</inputs>

	<outputs>
		<data format="txt" name="outputTxt" label="countNumber Output"/>
		<data name="outputTarFile" format="tar">
			<filter>tar</filter>
		</data>
	</outputs>

</tool>